void NoneLocalMeans::recompileOpenCLCode(Image::pointer input) {
    // Check if there is a need to recompile OpenCL code
    if(input->getDimensions() == mDimensionCLCodeCompiledFor &&
       input->getDataType() == mTypeCLCodeCompiledFor && !recompile)
        return;
    
    recompile = false;
    OpenCLDevice::pointer device = getMainDevice();
    std::string buildOptions = "";
    if(!device->isWritingTo3DTexturesSupported()) {
        buildOptions = "-DTYPE=" + getCTypeAsString(mOutputType);
    }
    buildOptions += " -D WINDOW=";
    buildOptions += std::to_string((windowSize-1)/2);
    buildOptions += " -D GROUP=";
    buildOptions += std::to_string((groupSize-1)/2);
    buildOptions += " -D KVERSION=";
    buildOptions += std::to_string(k);
    buildOptions += " -D EUCLID=";
    buildOptions += std::to_string(k);
    cl::Program program;
    if(input->getDimensions() == 2) {
        program = getOpenCLProgram(device, "2D", buildOptions);
    } else {
        //createOpenCLProgram(std::string(FAST_SOURCE_DIR) + "Algorithms/NoneLocalMeans/NoneLocalMeans3Dgs.cl", "3D");
        program = getOpenCLProgram(device, "3D", buildOptions);
    }
    mKernel = cl::Kernel(program, "noneLocalMeans");
    mDimensionCLCodeCompiledFor = input->getDimensions();
    mTypeCLCodeCompiledFor = input->getDataType();
}

void ImageImporter::execute() {
    if (mFilename == "")
        throw Exception("No filename was supplied to the ImageImporter");

    uchar* convertedPixelData;
    // Load image from disk using Qt
    QImage image;
    reportInfo() << "Trying to load image..." << Reporter::end();
    if(!image.load(mFilename.c_str())) {
        throw FileNotFoundException(mFilename);
    }
    reportInfo() << "Loaded image with size " << image.width() << " "  << image.height() << Reporter::end();

    QImage::Format format;
    if(mGrayscale) {
        format = QImage::Format_Grayscale8;
    } else {
        format = QImage::Format_RGB888;
    }
    QImage convertedImage = image.convertToFormat(format);

    // Get pixel data
    convertedPixelData = convertedImage.bits();

    Image::pointer output = getOutputData<Image>();
    std::cout << "image info" << std::endl;
    std::cout << convertedImage.width() << std::endl;
    std::cout << convertedImage.depth() << std::endl;
    std::cout << convertedImage.bytesPerLine() << std::endl;
    if(convertedImage.width()*convertedImage.depth()/8 != convertedImage.bytesPerLine()) {
        const int bytesPerPixel = (convertedImage.depth()/8);
        std::unique_ptr<uchar[]> fixedPixelData = std::make_unique<uchar[]>(image.width()*image.height());
        // Misalignment
        for(int scanline = 0; scanline < image.height(); ++scanline) {
            std::memcpy(
                    &fixedPixelData[scanline*image.width()*bytesPerPixel],
                    &convertedPixelData[scanline*convertedImage.bytesPerLine()],
                    image.width()*bytesPerPixel
            );
        }
        output->create(
            image.width(),
            image.height(),
            TYPE_UINT8,
            mGrayscale ? 1 : 3,
            getMainDevice(),
            fixedPixelData.get()
        );
    } else {
        output->create(
            image.width(),
            image.height(),
            TYPE_UINT8,
            mGrayscale ? 1 : 3,
            getMainDevice(),
            convertedPixelData
        );
    }
}

void BinaryThresholding::execute() {
    if(!mLowerThresholdSet && !mUpperThresholdSet) {
        throw Exception("BinaryThresholding need at least one threshold to be set.");
    }

    Image::pointer input = getStaticInputData<Image>(0);
    Segmentation::pointer output = getStaticOutputData<Segmentation>(0);

    output->createFromImage(input);

    if(getMainDevice()->isHost()) {
        throw Exception("Not implemented yet.");
    } else {
        OpenCLDevice::pointer device = OpenCLDevice::pointer(getMainDevice());
        cl::Program program;
        if(input->getDimensions() == 3) {
            program = getOpenCLProgram(device, "3D");
        } else {
            program = getOpenCLProgram(device, "2D");
        }
        cl::Kernel kernel;
        if(mLowerThresholdSet && mUpperThresholdSet) {
            kernel = cl::Kernel(program, "tresholding");
            kernel.setArg(3, mLowerThreshold);
            kernel.setArg(4, mUpperThreshold);
        } else if(mLowerThresholdSet) {
            kernel = cl::Kernel(program, "thresholdingWithOnlyLower");
            kernel.setArg(3, mLowerThreshold);
        } else {
            kernel = cl::Kernel(program, "thresholdingWithOnlyUpper");
            kernel.setArg(3, mUpperThreshold);
        }
        cl::NDRange globalSize;
        OpenCLImageAccess::pointer access = input->getOpenCLImageAccess(ACCESS_READ, device);
        if(input->getDimensions() == 2) {
            OpenCLImageAccess::pointer access2 = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
            kernel.setArg(0, *access->get2DImage());
            kernel.setArg(1, *access2->get2DImage());
            globalSize = cl::NDRange(output->getWidth(), output->getHeight());
        } else {
            // TODO no 3d image write support
            OpenCLImageAccess::pointer access2 = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
            kernel.setArg(0, *access->get3DImage());
            kernel.setArg(1, *access2->get3DImage());
            globalSize = cl::NDRange(output->getWidth(), output->getHeight(), output->getDepth());
        }
        kernel.setArg(2, (uchar)mLabel);

        cl::CommandQueue queue = device->getCommandQueue();
        queue.enqueueNDRangeKernel(
                kernel,
                cl::NullRange,
                globalSize,
                cl::NullRange
        );
    }
}

void executeAlgorithmOnHost(Image::pointer input, Image::pointer output) {
    ImageAccess inputAccess = input->getImageAccess(ACCESS_READ);
    ImageAccess outputAccess = output->getImageAccess(ACCESS_READ_WRITE);

    T * inputData = (T*)inputAccess.get();
    T * outputData = (T*)outputAccess.get();

    unsigned int nrOfElements = input->getWidth()*input->getHeight()*input->getDepth()*input->getNrOfComponents();
    for(unsigned int i = 0; i < nrOfElements; i++) {
        outputData[i] = 2.0*inputData[i];
    }
}

void SeededRegionGrowing::recompileOpenCLCode(Image::pointer input) {
    // Check if there is a need to recompile OpenCL code
    if(input->getDimensions() == mDimensionCLCodeCompiledFor &&
            input->getDataType() == mTypeCLCodeCompiledFor)
        return;

    OpenCLDevice::pointer device = getMainDevice();
    std::string buildOptions = "";
    if(input->getDataType() == TYPE_FLOAT) {
        buildOptions = "-DTYPE_FLOAT";
    } else if(input->getDataType() == TYPE_INT8 || input->getDataType() == TYPE_INT16) {
        buildOptions = "-DTYPE_INT";
    } else {
        buildOptions = "-DTYPE_UINT";
    }
    std::string filename;
    if(input->getDimensions() == 2) {
        filename = "Algorithms/SeededRegionGrowing/SeededRegionGrowing2D.cl";
    } else {
        filename = "Algorithms/SeededRegionGrowing/SeededRegionGrowing3D.cl";
    }
    int programNr = device->createProgramFromSource(std::string(FAST_SOURCE_DIR) + filename, buildOptions);
    mKernel = cl::Kernel(device->getProgram(programNr), "seededRegionGrowing");
    mDimensionCLCodeCompiledFor = input->getDimensions();
    mTypeCLCodeCompiledFor = input->getDataType();
}

void setScalarAsFloat(T* data, uint position, Image::pointer image, float value, uchar channel) {

    Vector3ui size = image->getSize();
    if(position >= size.x()*size.y()*size.z())
        throw OutOfBoundsException();

    uint address = position*image->getNrOfComponents() + channel;
    if(image->getDataType() == TYPE_SNORM_INT16) {
        data[address] = value * 32767.0f;;
    } else if(image->getDataType() == TYPE_UNORM_INT16) {
        data[address] = value * 65535.0f;;
    } else {
        data[address] = value;
    }
}

void ImageSlicer::execute() {
	Image::pointer input = getStaticInputData<Image>();
	Image::pointer output = getStaticOutputData<Image>();

	if(input->getDimensions() != 3)
		throw Exception("Image slicer can only be used for 3D images");

	if(!mArbitrarySlicing && !mOrthogonalSlicing)
		throw Exception("No slice plane given to the ImageSlicer");

	// TODO
	if(mOrthogonalSlicing) {
		orthogonalSlicing(input, output);
	} else {
		arbitrarySlicing(input, output);
	}
}

float getScalarAsFloat(T* data, uint position, Image::pointer image, uchar channel) {

    Vector3ui size = image->getSize();
    if(position >= size.x()*size.y()*size.z())
        throw OutOfBoundsException();

    T value = data[position*image->getNrOfComponents() + channel];
    float floatValue;
    if(image->getDataType() == TYPE_SNORM_INT16) {
        floatValue = std::max(-1.0f, (float)value / 32767.0f);
    } else if(image->getDataType() == TYPE_UNORM_INT16) {
        floatValue = (float)value / 65535.0f;
    } else {
        floatValue = value;
    }

    return floatValue;
}

void transferVTKDataToFAST(vtkImageData* image, Image::pointer output) {

    void* data;
    DataType type;
    switch(image->GetScalarType()) {
    case VTK_FLOAT:
        data = readVTKData<float>(image);
        type = TYPE_FLOAT;
        break;
    case VTK_CHAR:
    case VTK_SIGNED_CHAR:
        data = readVTKData<char>(image);
        type = TYPE_INT8;
        break;
    case VTK_UNSIGNED_CHAR:
        data = readVTKData<uchar>(image);
        type = TYPE_UINT8;
        break;
    case VTK_SHORT:
        data = readVTKData<short>(image);
        type = TYPE_INT16;
        break;
    case VTK_UNSIGNED_SHORT:
        data = readVTKData<ushort>(image);
        type = TYPE_UINT16;
        break;
    default:
        throw Exception("VTK image of unsupported type was supplied to the VTKImageImporter");
        break;
    }

    int * size = image->GetDimensions();
    if(image->GetDataDimension() == 2) {
        output->create(size[0]-1, size[1]-1,type,1,Host::getInstance(),data);
    } else if(image->GetDataDimension() == 3) {
        output->create(size[0]-1, size[1]-1,size[2]-1,type,1,Host::getInstance(),data);
    } else {
        throw Exception("Wrong number of dimensions in VTK image");
    }
    deleteArray(data, type);
}

void Dilation::execute() {
    Image::pointer input = getInputData<Image>();
    if(input->getDataType() != TYPE_UINT8) {
        throw Exception("Data type of image given to Dilation must be UINT8");
    }

    Image::pointer output = getOutputData<Image>();
    output->createFromImage(input);
    SceneGraph::setParentNode(output, input);
    output->fill(0);

    OpenCLDevice::pointer device = std::dynamic_pointer_cast<OpenCLDevice>(getMainDevice());
    cl::CommandQueue queue = device->getCommandQueue();
    cl::Program program = getOpenCLProgram(device);
    cl::Kernel dilateKernel(program, "dilate");

    Vector3ui size = input->getSize();

    OpenCLImageAccess::pointer access = input->getOpenCLImageAccess(ACCESS_READ, device);
    dilateKernel.setArg(0, *access->get3DImage());
    dilateKernel.setArg(2, mSize/2);

    if(!device->isWritingTo3DTexturesSupported()) {
        OpenCLBufferAccess::pointer access2 = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
        dilateKernel.setArg(1, *access2->get());

        queue.enqueueNDRangeKernel(
            dilateKernel,
            cl::NullRange,
            cl::NDRange(size.x(), size.y(), size.z()),
            cl::NullRange
        );
    } else {
        OpenCLImageAccess::pointer access2 = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);
        dilateKernel.setArg(1, *access2->get3DImage());

        queue.enqueueNDRangeKernel(
            dilateKernel,
            cl::NullRange,
            cl::NDRange(size.x(), size.y(), size.z()),
            cl::NullRange
        );
    }

}

static igtl::TransformMessage::Pointer createIGTLTransformMessage(Image::pointer image) {
    // Create transform message from the scene graph information of image
    igtl::Matrix4x4 matrix;
    AffineTransformation::pointer T = image->getSceneGraphNode()->getTransformation();
    for(int i = 0; i < 4; i++) {
    for(int j = 0; j < 4; j++) {
        matrix[i][j] = T->getTransform().matrix()(i,j);
    }}

    igtl::TransformMessage::Pointer message = igtl::TransformMessage::New();
    message->SetDeviceName("DummyTransform");
    message->SetMatrix(matrix);

    return message;
}

void
SegmentationRenderer::draw(Matrix4f perspectiveMatrix, Matrix4f viewingMatrix, float zNear, float zFar, bool mode2D) {
    std::lock_guard<std::mutex> lock(mMutex);
    OpenCLDevice::pointer device = std::dynamic_pointer_cast<OpenCLDevice>(getMainDevice());


    if(mColorsModified) {
        // Transfer colors to device (this doesn't have to happen every render call..)
        std::unique_ptr<float[]> colorData(new float[3*mLabelColors.size()]);
        std::unordered_map<int, Color>::iterator it;
        for(it = mLabelColors.begin(); it != mLabelColors.end(); it++) {
            colorData[it->first*3] = it->second.getRedValue();
            colorData[it->first*3+1] = it->second.getGreenValue();
            colorData[it->first*3+2] = it->second.getBlueValue();
        }

        mColorBuffer = cl::Buffer(
                device->getContext(),
                CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR,
                sizeof(float)*3*mLabelColors.size(),
                colorData.get()
        );
    }

    if(mFillAreaModified) {
        // Transfer colors to device (this doesn't have to happen every render call..)
        std::unique_ptr<char[]> fillAreaData(new char[mLabelColors.size()]);
        std::unordered_map<int, Color>::iterator it;
        for(it = mLabelColors.begin(); it != mLabelColors.end(); it++) {
            if(mLabelFillArea.count(it->first) == 0) {
                // Use default value
                fillAreaData[it->first] = mFillArea;
            } else {
                fillAreaData[it->first] = mLabelFillArea[it->first];
            }
        }

        mFillAreaBuffer = cl::Buffer(
                device->getContext(),
                CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR,
                sizeof(char)*mLabelColors.size(),
                fillAreaData.get()
        );
    }

    mKernel = cl::Kernel(getOpenCLProgram(device), "renderToTexture");
    mKernel.setArg(2, mColorBuffer);
    mKernel.setArg(3, mFillAreaBuffer);
    mKernel.setArg(4, mBorderRadius);
    mKernel.setArg(5, mOpacity);


    for(auto it : mDataToRender) {
        Image::pointer input = std::static_pointer_cast<Image>(it.second);
        uint inputNr = it.first;

        if(input->getDimensions() != 2)
            throw Exception("SegmentationRenderer only supports 2D images. Use ImageSlicer to extract a 2D slice from a 3D image.");

        if(input->getDataType() != TYPE_UINT8)
            throw Exception("SegmentationRenderer only support images with dat type uint8.");

        // Check if a texture has already been created for this image
        if(mTexturesToRender.count(inputNr) > 0 && mImageUsed[inputNr] == input)
            continue; // If it has already been created, skip it

        // If it has not been created, create the texture

        OpenCLImageAccess::pointer access = input->getOpenCLImageAccess(ACCESS_READ, device);
        cl::Image2D *clImage = access->get2DImage();

        // Run kernel to fill the texture
        cl::CommandQueue queue = device->getCommandQueue();

        if (mTexturesToRender.count(inputNr) > 0) {
            // Delete old texture
            glDeleteTextures(1, &mTexturesToRender[inputNr]);
            mTexturesToRender.erase(inputNr);
            glDeleteVertexArrays(1, &mVAO[inputNr]);
            mVAO.erase(inputNr);
        }

        cl::Image2D image;
        cl::ImageGL imageGL;
        std::vector<cl::Memory> v;
        GLuint textureID;
        // TODO The GL-CL interop here is causing glClear to not work on AMD systems and therefore disabled
        /*
        if(DeviceManager::isGLInteropEnabled()) {
            // Create OpenGL texture
            glGenTextures(1, &textureID);
            glBindTexture(GL_TEXTURE_2D, textureID);
            glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
            glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
            glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, input->getWidth(), input->getHeight(), 0, GL_RGBA, GL_FLOAT, 0);

            // Create CL-GL image
            imageGL = cl::ImageGL(
                    device->getContext(),
                    CL_MEM_READ_WRITE,
//.........这里部分代码省略.........

void executeAlgorithmOnHost(Image::pointer input, Image::pointer output, unsigned char group, unsigned char window, float strength, unsigned char sigma) {
	throw Exception("This is on host, does not work atm");
    
    ImageAccess::pointer inputAccess = input->getImageAccess(ACCESS_READ);
    ImageAccess::pointer outputAccess = output->getImageAccess(ACCESS_READ_WRITE);

    T * inputData = (T*)inputAccess->get();
    T * outputData = (T*)outputAccess->get();

    unsigned int width = input->getWidth();
    unsigned int height = input->getHeight();
    //Window is window-1/2
    //group is group-1/2
    //strength is strength*strength
    //sigma is sigma*sigma
    //Not working atm with the T
    //Does not work with outofbounds atm
    //So this code is for all pixels inbound, meaning x + group + window < width / x - group - window > 0 //same for y
    for (int x = 0; x < width; x++){
        for (int y = 0; y < height; y++){
            
            double normSum = 0.0;
            double totSum = 0.0;
            double indi = 0.0;
            double groupTot = 0.0;
            double value = 0.0;

            for (int i = x - window; i <= x + window; i++){
                for (int j = y - window; j <= y + window; j++){
                    if (i != x && j != y){

                        int mX = x - group;
                        int mY = y - group;
                        for (int k = i - group; k <= i + group; k++, mX++){
                            for (int l = j - group; l <= j + group; l++, mY++){
                                //This is wrong, need to fix T
                                //indi = inputData[mX][mY] - inputData[k][l];
                                indi = abs(indi*indi);
                                indi = exp( - (indi/strength));
                                groupTot += indi;
                            }
                        }
                        //This is wrong, need to fix T
                        //value = inputData[i][j];
                        double pA[] = {i,j};
                        double pB[] = {x,y};
                        //double dist = i, j - x, y;
                        double dist = std::inner_product(std::begin(pA), std::end(pA), std::begin(pB), 0.0);
                        
                        double gaussWeight = exp(-(dist / (2.0 * sigma)));
                        gaussWeight = gaussWeight / (2.0 * sigma);
                        groupTot *= gaussWeight;

                        normSum += groupTot;
                        totSum += groupTot * value;
                        groupTot = 0.0;
                    }
                }
            }
            value = totSum / normSum;
            /*
            Not sure it needed
            if (value < 0){
                value = 0;
            }
            if (value > 1.0){
                value = 1.0f;
            }
            */
            //This is wrong, need to fix T
            //outputData[x][y] = (T)value;
            
        }
    }
}

static igtl::ImageMessage::Pointer createIGTLImageMessage(Image::pointer image) {
    // size parameters
    int   size[3]     = {(int)image->getWidth(), (int)image->getHeight(), (int)image->getDepth()};       // image dimension
    float spacing[3]  = {image->getSpacing().x(), image->getSpacing().y(), image->getSpacing().z()};     // spacing (mm/pixel)
    int   svoffset[3] = {0, 0, 0};           // sub-volume offset
    int   scalarType;
    size_t totalSize = image->getWidth()*image->getHeight()*image->getDepth()*image->getNrOfChannels();
    switch(image->getDataType()) {
        case TYPE_UINT8:
            scalarType = igtl::ImageMessage::TYPE_UINT8;
            totalSize *= sizeof(unsigned char);
            break;
        case TYPE_INT8:
            scalarType = igtl::ImageMessage::TYPE_INT8;
            totalSize *= sizeof(char);
            break;
        case TYPE_UINT16:
            scalarType = igtl::ImageMessage::TYPE_UINT16;
            totalSize *= sizeof(unsigned short);
            break;
        case TYPE_INT16:
            scalarType = igtl::ImageMessage::TYPE_INT16;
            totalSize *= sizeof(short);
            break;
        case TYPE_FLOAT:
            scalarType = igtl::ImageMessage::TYPE_FLOAT32;
            totalSize *= sizeof(float);
            break;
    }

    //------------------------------------------------------------
    // Create a new IMAGE type message
    igtl::ImageMessage::Pointer imgMsg = igtl::ImageMessage::New();
    imgMsg->SetDimensions(size);
    imgMsg->SetSpacing(spacing);
    imgMsg->SetNumComponents(image->getNrOfChannels());
    imgMsg->SetScalarType(scalarType);
    imgMsg->SetDeviceName("DummyImage");
    imgMsg->SetSubVolume(size, svoffset);
    imgMsg->AllocateScalars();

    ImageAccess::pointer access = image->getImageAccess(ACCESS_READ);
    memcpy(imgMsg->GetScalarPointer(), access->get(), totalSize);

    return imgMsg;
}

void MetaImageImporter::execute() {
    if(mFilename == "")
        throw Exception("Filename was not set in MetaImageImporter");

    // Open and parse mhd file
    std::fstream mhdFile;
    mhdFile.open(mFilename.c_str(), std::fstream::in);
    if(!mhdFile.is_open())
        throw FileNotFoundException(mFilename);
    std::string line;
    std::string rawFilename;
    bool sizeFound = false,
         rawFilenameFound = false,
         typeFound = false,
         dimensionsFound = false;
    std::string typeName;

    // Find NDims first
    bool imageIs3D = false;
    do {
        std::getline(mhdFile, line);
        if(line.substr(0, 5) == "NDims") {
            if(line.substr(5+3, 1) == "3") {
                imageIs3D = true;
            } else if(line.substr(5+3, 1) == "2") {
                imageIs3D = false;
            }
            dimensionsFound = true;
        }
    } while(!mhdFile.eof() && !dimensionsFound);

    if(!dimensionsFound)
        throw Exception("NDims not found in metaimage file.");

    // Reset and start reading file from beginning
    mhdFile.seekg(0);

    unsigned int width, height, depth = 1;
    unsigned int nrOfComponents = 1;
    Image::pointer output = getOutputData<Image>(0);

    Vector3f spacing(1,1,1), offset(0,0,0), centerOfRotation(0,0,0);
    Matrix3f transformMatrix = Matrix3f::Identity();
    bool isCompressed = false;
    std::size_t compressedDataSize = 0;

    do{
        std::getline(mhdFile, line);
        boost::trim(line);
        if(line.size() == 0) // line is empty
            continue;
        int firstSpace = line.find(" ");
        std::string key = line.substr(0, firstSpace);
        boost::trim(key);
        int equalSignPos = line.find("=");
        std::string value = line.substr(equalSignPos+1);
        boost::trim(value);
        if(key == "DimSize") {
            std::vector<std::string> values;
            boost::split(values, value, boost::is_any_of(" "));
            // Remove any empty values:
            values.erase(std::remove(values.begin(), values.end(), ""), values.end());

            if(imageIs3D) {
                if(values.size() != 3)
                    throw Exception("DimSize in MetaImage file did not contain 3 numbers");
                depth = boost::lexical_cast<int>(values[2]);
            } else {
                if(values.size() != 2)
                    throw Exception("DimSize in MetaImage file did not contain 2 numbers");
            }
            width = boost::lexical_cast<int>(values[0]);
            height = boost::lexical_cast<int>(values[1]);
            sizeFound = true;
        } else if(key == "CompressedData" && value == "True") {
            isCompressed = true;
        } else if(key == "CompressedDataSize") {
            compressedDataSize = boost::lexical_cast<int>(value);
        } else if(key == "ElementDataFile") {
            rawFilename = value;
            rawFilenameFound = true;

            // Remove any trailing spaces
            int pos = rawFilename.find(" ");
            if(pos > 0)
            rawFilename = rawFilename.substr(0,pos);

            // Get path name
            pos = mFilename.rfind('/');
            if(pos > 0)
                rawFilename = mFilename.substr(0,pos+1) + rawFilename;
        } else if(key == "ElementType") {
            typeFound = true;
            typeName = value;

            // Remove any trailing spaces
            int pos = typeName.find(" ");
            if(pos > 0)
            typeName = typeName.substr(0,pos);

//.........这里部分代码省略.........

void DoubleFilter::execute() {
    if(!mInput.isValid()) {
        throw Exception("No input supplied to GaussianSmoothingFilter");
    }

    Image::pointer input = mInput;
    Image::pointer output = mOutput;

    // Initialize output image
    output->createFromImage(input, mDevice);

    if(mDevice->isHost()) {
        // Execution device is Host, use the executeAlgorithmOnHost function with the given data type
        switch(input->getDataType()) {
            // This macro creates a case statement for each data type and sets FAST_TYPE to the correct C++ data type
            fastSwitchTypeMacro(executeAlgorithmOnHost<FAST_TYPE>(input, output));
        }
    } else {
        // Execution device is an OpenCL device
        OpenCLDevice::pointer device = boost::static_pointer_cast<OpenCLDevice>(mDevice);

        // Set build options based on the data type of the data
        std::string buildOptions = "";
        switch(input->getDataType()) {
        case TYPE_FLOAT:
            buildOptions = "-DTYPE=float";
            break;
        case TYPE_INT8:
            buildOptions = "-DTYPE=char";
            break;
        case TYPE_UINT8:
            buildOptions = "-DTYPE=uchar";
            break;
        case TYPE_INT16:
            buildOptions = "-DTYPE=short";
            break;
        case TYPE_UINT16:
            buildOptions = "-DTYPE=ushort";
            break;
        }

        // Compile the code
        int programNr = device->createProgramFromSource(std::string(FAST_SOURCE_DIR) + "Tests/Algorithms/DoubleFilter.cl", buildOptions);
        cl::Kernel kernel = cl::Kernel(device->getProgram(programNr), "doubleFilter");

        // Get global size for the kernel
        cl::NDRange globalSize(input->getWidth()*input->getHeight()*input->getDepth()*input->getNrOfComponents());

        // Set the arguments for the kernel
        OpenCLBufferAccess inputAccess = input->getOpenCLBufferAccess(ACCESS_READ, device);
        OpenCLBufferAccess outputAccess = output->getOpenCLBufferAccess(ACCESS_READ_WRITE, device);
        kernel.setArg(0, *inputAccess.get());
        kernel.setArg(1, *outputAccess.get());

        // Execute the kernel
        device->getCommandQueue().enqueueNDRangeKernel(
                kernel,
                cl::NullRange,
                globalSize,
                cl::NullRange
        );
    }

    // Update timestamp of the output data
    output->updateModifiedTimestamp();
}

void ImageSlicer::orthogonalSlicing(Image::pointer input, Image::pointer output) {
    OpenCLDevice::pointer device = getMainDevice();

    // Determine slice nr and width and height
    unsigned int sliceNr;
    if(mOrthogonalSliceNr < 0) {
        switch(mOrthogonalSlicePlane) {
        case PLANE_X:
            sliceNr = input->getWidth()/2;
            break;
        case PLANE_Y:
            sliceNr = input->getHeight()/2;
            break;
        case PLANE_Z:
            sliceNr = input->getDepth()/2;
            break;
        }
    } else {
        // Check that mSliceNr is valid
        sliceNr = mOrthogonalSliceNr;
        switch(mOrthogonalSlicePlane) {
        case PLANE_X:
            if(sliceNr >= input->getWidth())
                sliceNr = input->getWidth()-1;
            break;
        case PLANE_Y:
            if(sliceNr >= input->getHeight())
                sliceNr = input->getHeight()-1;
            break;
        case PLANE_Z:
            if(sliceNr >= input->getDepth())
                sliceNr = input->getDepth()-1;
            break;
        }
    }
    unsigned int slicePlaneNr, width, height;
    Vector3f spacing(0,0,0);
    switch(mOrthogonalSlicePlane) {
        case PLANE_X:
            slicePlaneNr = 0;
            width = input->getHeight();
            height = input->getDepth();
            spacing.x() = input->getSpacing().y();
            spacing.y() = input->getSpacing().z();
            break;
        case PLANE_Y:
            slicePlaneNr = 1;
            width = input->getWidth();
            height = input->getDepth();
            spacing.x() = input->getSpacing().x();
            spacing.y() = input->getSpacing().z();
            break;
        case PLANE_Z:
            slicePlaneNr = 2;
            width = input->getWidth();
            height = input->getHeight();
            spacing.x() = input->getSpacing().x();
            spacing.y() = input->getSpacing().y();
            break;
    }

    output->create(width, height, input->getDataType(), input->getNrOfComponents());
    output->setSpacing(spacing);

    OpenCLImageAccess::pointer inputAccess = input->getOpenCLImageAccess(ACCESS_READ, device);
    OpenCLImageAccess::pointer outputAccess = output->getOpenCLImageAccess(ACCESS_READ_WRITE, device);

	cl::CommandQueue queue = device->getCommandQueue();
	cl::Program program = getOpenCLProgram(device);
	cl::Kernel kernel(program, "orthogonalSlicing");

    kernel.setArg(0, *inputAccess->get3DImage());
    kernel.setArg(1, *outputAccess->get2DImage());
    kernel.setArg(2, sliceNr);
    kernel.setArg(3, slicePlaneNr);
    queue.enqueueNDRangeKernel(
            kernel,
            cl::NullRange,
            cl::NDRange(width, height),
            cl::NullRange
    );

    // TODO set scene graph transformation
}

#include "catch.hpp"
#include "VTKImageImporter.hpp"
#include "VTKImageExporter.hpp"
#include "ImageImporter.hpp"

using namespace fast;

// TODO rewrite this test so that it doesn't use the vtk exporter
TEST_CASE("Import an image from VTK to FAST", "[fast][VTK]") {
    ImageImporter::pointer importer = ImageImporter::New();
    importer->setFilename(std::string(FAST_TEST_DATA_DIR) + "US-2D.jpg");
    Image::pointer fastImage = importer->getOutput();

    // VTK Export
    vtkSmartPointer<VTKImageExporter> vtkExporter = VTKImageExporter::New();
    vtkExporter->SetInput(fastImage);
    vtkSmartPointer<vtkImageData> vtkImage = vtkExporter->GetOutput();
    vtkExporter->Update();

    // VTK Import example
    VTKImageImporter::pointer vtkImporter = VTKImageImporter::New();
    vtkImporter->setInput(vtkImage);
    Image::pointer importedImage = vtkImporter->getOutput();
    vtkImporter->update();

    CHECK(fastImage->getWidth() == importedImage->getWidth());
    CHECK(fastImage->getHeight() == importedImage->getHeight());
    CHECK(fastImage->getDepth() == 1);
    CHECK(fastImage->getDimensions() == 2);
    CHECK(fastImage->getDataType() == TYPE_FLOAT);
}

void ManualImageStreamer::producerStream() {
    uint i = mStartNumber;
    int replays = 0;
    uint64_t previousTimestamp = 0;
    auto previousTimestampTime = std::chrono::high_resolution_clock::time_point::min();
    int currentSequence = 0;
    while(true) {
        {
            std::unique_lock<std::mutex> lock(mStopMutex);
            if(mStop) {
                mStreamIsStarted = false;
                mFirstFrameIsInserted = false;
                mHasReachedEnd = false;
                break;
            }
        }
        try {
            Image::pointer image = mImages[currentSequence].at(i);
            addOutputData(0, image);
            if(image->getCreationTimestamp() != 0) {
                uint64_t timestamp = image->getCreationTimestamp();
                // Wait as long as necessary before adding image
                // Time passed since last frame
                auto timePassed = std::chrono::duration_cast<std::chrono::milliseconds>(
                        std::chrono::high_resolution_clock::now() - previousTimestampTime);
                while (timestamp > previousTimestamp + timePassed.count()) {
                    // Wait
                    int64_t left = (timestamp - previousTimestamp) - timePassed.count();
                    reportInfo() << "Sleeping for " << left << " ms" << reportEnd();
                    std::this_thread::sleep_for(std::chrono::milliseconds(left));
                    timePassed = std::chrono::duration_cast<std::chrono::milliseconds>(
                            std::chrono::high_resolution_clock::now() - previousTimestampTime);
                }
                previousTimestamp = timestamp;
                previousTimestampTime = std::chrono::high_resolution_clock::now();
            }
            if(mSleepTime > 0)
                std::this_thread::sleep_for(std::chrono::milliseconds(mSleepTime));
            if(!mFirstFrameIsInserted) {
                {
                    std::lock_guard<std::mutex> lock(mFirstFrameMutex);
                    mFirstFrameIsInserted = true;
                }
                mFirstFrameCondition.notify_one();
            }
            mNrOfFrames++;
            i += mStepSize;
        } catch(std::out_of_range &e) {
            if(i > 0) {
                reportInfo() << "Reached end of stream" << Reporter::end();
                // If there where no files found at all, we need to release the execute method
                if(!mFirstFrameIsInserted) {
                    {
                        std::lock_guard<std::mutex> lock(mFirstFrameMutex);
                        mFirstFrameIsInserted = true;
                    }
                    mFirstFrameCondition.notify_one();
                }
                if(mLoop || (mNrOfReplays > 0 && replays != mNrOfReplays || (currentSequence < mImages.size()-1))) {
                    // Restart stream
                    previousTimestamp = 0;
                    previousTimestampTime = std::chrono::high_resolution_clock::time_point::min();
                    replays++;
                    i = mStartNumber;
                    currentSequence++;
                    // Go to first sequence if looping is enabled
                    if(mLoop && currentSequence == mImages.size()) {
                        currentSequence = 0;
                    }
                    continue;
                }
                mHasReachedEnd = true;
                // Reached end of stream
                break;
            } else {
                throw e;
            }
        }
    }
}